The complexity of IFNB1 enhanceosome formation prior to transcription initiation is assumed to provide the dominant contribution to the stochastic behavior. This assembly involves binding of NFKB, AP-1, IRF, and HMG-I(Y) to form the enhanceosome.
We denote HMG-I(Y) by P1, NFKB by P2, AP1 by P3 and the IRFs by P4. The model comprises four proteins P1, P2, P3 and P4 that bind without interacting, and represent the corresponding cooperative behavior through protein binding in a well-defined order.
The relevant reactions are given by:

where D1 represents promoter region of allele 1. One has a similar set of equations for promoter region D2 of allele 2 where we have used the same reaction rate constants since the alleles are assumed to be functionally identical.